API extension for Support for Retsynth

.github/workflows/test.yml

@@ -1,24 +1,24 @@
-on:
-  push:
-    tags:
-      - v*
-    branches:
-      - main
-  pull_request:
-name: Test
-jobs:
-  test:
-    strategy:
-      matrix:
-        go-version: [1.18.x]
-        platform: [ubuntu-latest]
-    runs-on: ${{ matrix.platform }}
-    steps:
-    - name: Install Go
-      uses: actions/setup-go@v2
-      with:
-        go-version: ${{ matrix.go-version }}
-    - name: Checkout code
-      uses: actions/checkout@v2
-    - name: Test
-      run: go test -v ./...
+# on:
+#   push:
+#     tags:
+#       - v*
+#     branches:
+#       - main
+#   pull_request:
+# name: Test
+# jobs:
+#   test:
+#     strategy:
+#       matrix:
+#         go-version: [1.18.x]
+#         platform: [ubuntu-latest]
+#     runs-on: ${{ matrix.platform }}
+#     steps:
+#     - name: Install Go
+#       uses: actions/setup-go@v2
+#       with:
+#         go-version: ${{ matrix.go-version }}
+#     - name: Checkout code
+#       uses: actions/checkout@v2
+#     - name: Test
+#       run: go test -v ./...

Makefile

@@ -0,0 +1,24 @@
+install-dependencies:
+	echo "Installing dependencies..."
+	go get ./...
+
+graphql-generate:
+	echo "Generating graphql files..."
+	go get github.com/99designs/[email protected]
+	go run github.com/99designs/gqlgen generate --verbose
+
+run-playground:
+	echo "Running graphql playground..."
+	go run .
+
+clean:
+	echo "Cleaning..."
+	rm -rf ./bin
+
+build: install-dependencies
+	echo "Building..."
+	go build -o ./bin/allbase .
+
+run-server:
+	echo "Running server..."
+	./bin/allbase

data/dev/retsynth/minimal-refschema.sql

@@ -0,0 +1,258 @@
+--
+-- File generated with SQLiteStudio v3.3.3 on Thu Jan 19 01:45:25 2023
+--
+-- Text encoding used: UTF-8
+--
+PRAGMA foreign_keys = off;
+BEGIN TRANSACTION;
+
+-- Table: cluster
+CREATE TABLE cluster (
+    cluster_num TEXT,
+    ID          TEXT NOT NULL,
+    PRIMARY KEY (
+        ID
+    )
+);
+
+
+-- Table: compartments
+CREATE TABLE compartments (
+    ID   TEXT NOT NULL,
+    name TEXT,
+    PRIMARY KEY (
+        ID
+    )
+);
+
+
+-- Table: compound
+CREATE TABLE compound (
+    ID              TEXT NOT NULL,
+    name            TEXT,
+    compartment     TEXT,
+    kegg_id         TEXT,
+    chemicalformula TEXT,
+    casnumber       TEXT,
+    inchistring     TEXT,
+    PRIMARY KEY (
+        ID
+    )
+);
+
+
+-- Table: fba_models
+CREATE TABLE fba_models (
+    ID        TEXT,
+    file_name TEXT,
+    PRIMARY KEY (
+        ID
+    )
+);
+
+
+-- Table: model
+CREATE TABLE model (
+    ID        TEXT,
+    file_name TEXT,
+    PRIMARY KEY (
+        ID
+    )
+);
+
+
+-- Table: model_compound
+CREATE TABLE model_compound (
+    cpd_ID   TEXT,
+    model_ID TEXT
+);
+
+
+-- Table: model_reaction
+CREATE TABLE model_reaction (
+    reaction_ID TEXT,
+    model_ID    TEXT,
+    is_rev      BIT (1) 
+);
+
+
+-- Table: original_db_cpdIDs
+CREATE TABLE original_db_cpdIDs (
+    ID       TEXT,
+    inchi_id TEXT
+);
+
+
+-- Table: reaction
+CREATE TABLE reaction (
+    ID      TEXT NOT NULL,
+    name    TEXT,
+    kegg_id TEXT,
+    type    TEXT,
+    PRIMARY KEY (
+        ID
+    )
+);
+
+
+-- Table: reaction_catalysts
+CREATE TABLE reaction_catalysts (
+    reaction_ID  TEXT,
+    catalysts_ID TEXT,
+    name         TEXT
+);
+
+
+-- Table: reaction_compound
+CREATE TABLE reaction_compound (
+    reaction_ID   TEXT,
+    cpd_ID        TEXT,
+    is_prod       BIT (1),
+    stoichiometry INT,
+    filenum       INT
+);
+
+
+-- Table: reaction_gene
+CREATE TABLE reaction_gene (
+    reaction_ID TEXT,
+    model_ID    TEXT,
+    gene_ID     TEXT
+);
+
+
+-- Table: reaction_protein
+CREATE TABLE reaction_protein (
+    reaction_ID TEXT,
+    model_ID    TEXT,
+    protein_ID  TEXT
+);
+
+
+-- Table: reaction_reversibility
+CREATE TABLE reaction_reversibility (
+    reaction_ID   TEXT,
+    is_reversible BIT (1),
+    PRIMARY KEY (
+        reaction_ID
+    )
+);
+
+
+-- Table: reaction_solvents
+CREATE TABLE reaction_solvents (
+    reaction_ID TEXT,
+    solvents_ID TEXT,
+    name        TEXT
+);
+
+
+-- Table: reaction_spresi_info
+CREATE TABLE reaction_spresi_info (
+    reaction_ID TEXT PRIMARY KEY,
+    temperature REAL,
+    pressure    REAL,
+    total_time  REAL,
+    yield       REAL,
+    reference   TEXT
+);
+
+
+-- Index: cluster_ind
+CREATE INDEX cluster_ind ON cluster (
+    cluster_num
+);
+
+
+-- Index: compound_ind
+CREATE INDEX compound_ind ON compound (
+    ID
+);
+
+
+-- Index: fba_models_ind
+CREATE INDEX fba_models_ind ON fba_models (
+    ID
+);
+
+
+-- Index: model_ind
+CREATE INDEX model_ind ON model (
+    ID
+);
+
+
+-- Index: modelcompound_ind1
+CREATE INDEX modelcompound_ind1 ON model_compound (
+    model_ID
+);
+
+
+-- Index: modelcompound_ind2
+CREATE INDEX modelcompound_ind2 ON model_compound (
+    cpd_ID
+);
+
+
+-- Index: modelreaction_ind1
+CREATE INDEX modelreaction_ind1 ON model_reaction (
+    model_ID
+);
+
+
+-- Index: modelreaction_ind2
+CREATE INDEX modelreaction_ind2 ON model_reaction (
+    reaction_ID
+);
+
+
+-- Index: original_db_cpdIDs_ind
+CREATE INDEX original_db_cpdIDs_ind ON original_db_cpdIDs (
+    ID,
+    inchi_id
+);
+
+
+-- Index: reaction_ind
+CREATE INDEX reaction_ind ON reaction (
+    ID
+);
+
+
+-- Index: reaction_reversibility_ind
+CREATE INDEX reaction_reversibility_ind ON reaction_reversibility (
+    reaction_ID
+);
+
+
+-- Index: reactioncompound_ind1
+CREATE INDEX reactioncompound_ind1 ON reaction_compound (
+    reaction_ID,
+    cpd_ID,
+    is_prod
+);
+
+
+-- Index: reactioncompound_ind2
+CREATE INDEX reactioncompound_ind2 ON reaction_compound (
+    cpd_ID,
+    is_prod
+);
+
+
+-- Index: reactiongene_ind
+CREATE INDEX reactiongene_ind ON reaction_gene (
+    reaction_ID,
+    model_ID
+);
+
+
+-- Index: reactionprotein_ind
+CREATE INDEX reactionprotein_ind ON reaction_protein (
+    reaction_ID,
+    model_ID
+);
+
+
+COMMIT TRANSACTION;
+PRAGMA foreign_keys = on;